I'm thinking about replacing my Pentium d and my mobo with intel core i5650 and of course a compatible mobo?

Integrated graphics cards, while they have gotten better in recent years, still lack power in comparison to PCI express graphics cards(like your 9400gt). I would suggest upgrading the card, although not necessary, to something a little more powerful, like a 9800. Don't go overboard with cards like the GTS 400, and GTS 500. In answer to your question, neither. Yes, you can switch between the two, but not in the same sense as the laptops with switchable graphics. Most Laptops allow switching in real time, whereas the desktop motherboard will require a settings change in the BIOS.